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Updated: Jul 8, 2026
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
Syed Hussain Ather1, Olaitan Igbagbo Awe2, Thomas J Butler3
1National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
F1000Research
|October 6, 2020
Summary
SeqAcademy is a user-friendly markdown pipeline for analyzing RNA sequencing (RNA-Seq) and ChIP sequencing (ChIP-Seq) data. This tutorial introduces novice bioinformaticians to essential tools for biological insight from sequencing reads.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Gene expression quantification and transcript structure characterization are key molecular biology challenges.
- RNA sequencing (RNA-Seq) and ChIP sequencing (ChIP-Seq) are powerful but complex methods for beginners.
- Existing pipelines often cater to advanced users, leaving a gap for novices.
Purpose of the Study:
- To present SeqAcademy, a comprehensive tutorial for analyzing RNA-Seq and ChIP-Seq data.
- To provide a user-friendly, start-to-finish pipeline for novice bioinformaticians.
- To facilitate the analysis of public RNA-Seq and ChIP-Seq data.
Main Methods:
- Developed a pipeline entirely in markdown language.
- Integrated popular bioinformatics tools for RNA-Seq and ChIP-Seq analysis.
- Utilized publicly available sequencing data and a yeast experiment for demonstration.
Main Results:
- SeqAcademy offers a step-by-step guide from raw reads to biological insights.
- The pipeline emphasizes practical and conceptual aspects of data analysis.
- It bridges the gap between complex tools and novice users.
Conclusions:
- SeqAcademy effectively introduces state-of-the-art RNA-Seq and ChIP-Seq analysis tools.
- This resource empowers beginning bioinformaticians to analyze large public datasets.
- It facilitates broader accessibility to genomic data analysis.
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